Genome Biology | Volume 7 Issue 6

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	Volume 7 Issue 6
	Comment
	Comment The ninth wave Gregory A Petsko Genome Biology 2006, 7:109 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New, all-pervading technologies, such as the web and genomics, are like the 'ninth waves' of surfboard riders, washing over our culture with sudden, transforming power. The danger is that quality is reduced as we deal with the flood of data.
	Review
	Protein family review The MAP1 family of microtubule-associated proteins Shelley Halpain, Leif Dehmelt Genome Biology 2006, 7:224 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MAP1-family proteins are classical microtubule-associated proteins (MAPs) that bind along the microtubule lattice and stabilize microtubules.
	Minireview Protein synthesis molecule by molecule Ido Golding, Edward C Cox Genome Biology 2006, 7:221 (20 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Even a seemingly uniform culture of bacteria is made up of cells very different from each other in terms of their levels of a given protein. This individuality has now finally been quantified at single-molecule resolution.
	Minireview The subcellular localization of the mammalian proteome comes a fraction closer Jeremy C Simpson, Rainer Pepperkok Genome Biology 2006, 7:222 (23 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study shows the successful application of protein correlation profiling to the subcellular localization of organelle proteins in mammalian cells.
	Minireview The elusive yeast interactome Johannes Goll, Peter Uetz Genome Biology 2006, 7:223 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two comprehensive studies of the total complement of protein complexes in yeast come up with surprisingly different answers.
	Opinion Viruses take center stage in cellular evolution Jean-Michel Claverie Genome Biology 2006, 7:110 (16 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Advances in genomics have stimulated new hypotheses that DNA viruses were the origin of the eukaryotic cell nucleus, and that they should be considered as living things.
	Report
	Meeting report Is there gold at the top of the beanstalk? Michael A Djordjevic, Charles Buer Genome Biology 2006, 7:318 (23 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 3rd International Legume Genetics and Genomics Conference, Brisbane, Australia, 9-13 April 2006.
	Meeting report Chromatin remodeling and genome stability Gráinne Barkess Genome Biology 2006, 7:319 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 12th Tenovus Scotland Symposium 'Stability and Regulation of Genes and Genomes', Glasgow UK, 6-7 April 2006.
	Meeting report Mobile DNA: genomes under the influence Cédric Feschotte, Ellen J Pritham Genome Biology 2006, 7:320 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the American Society for Microbiology Conference on Mobile DNA, Banff, Canada, 24 February-1 March 2006.
	Research
	Research Analysis of gene expression in operons of Streptomyces coelicolor Emma Laing, Vassilis Mersinias, Colin P Smith, Simon J Hubbard Genome Biology 2006, 7:R46 (2 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the relative transcript levels of intra-operonic genes in Streptomyces coelicolor suggests significant levels of internal regulation.
	Research Slow, stochastic transgene repression with properties of a timer Clifford L Wang, Desirée C Yang, Matthias Wabl Genome Biology 2006, 7:R47 (9 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The dynamics of retroviral transgene repression were analyzed in several clones; repression was found to be slow and different genomic positions showed different dynamics.
	Research What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Diana Ekman, Sara Light, Åsa K Björklund, Arne Elofsson Genome Biology 2006, 7:R45 (16 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of hubs (proteins with many interactors) and non-hubs in the S. cerevisiae protein interaction network shows that hub proteins are enriched with multiple and repeated domains.
	Research Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling Daniel E Zak, Haiping Hao, Rajanikanth Vadigepalli, Gregory M Miller, Babatunde A Ogunnaike, James S Schwaber Genome Biology 2006, 7:R48 (19 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A systems level analysis of circadian time-dependent signaling via the epidermal growth factor receptor in the suprachiasmatic nucleus suggests several transcription factors that mediate the transcriptional response to epidermal growth factor receptor signaling.
	Research Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system Lyris MF de Godoy, Jesper V Olsen, Gustavo A de Souza, Guoqing Li, Peter Mortensen, Matthias Mann Genome Biology 2006, 7:R50 (19 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A mass spectrometry analysis of the yeast proteome shows that complex mixture analysis is not limited by sensitivity but by a combination of dynamic range and by effective sequencing speed.
	Research Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses Nalini Polavarapu, Nathan J Bowen, John F McDonald Genome Biology 2006, 7:R51 (28 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification and characterization of 42 families of chimpanzee endogenous retroviruses and a comparison to their human orthologs is described.
	Research Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence Ian J Donaldson, Berthold Göttgens Genome Biology 2006, 7:R52 (29 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-wide identification of conserved candidate transcription-factor binding sites that have evolved since the human-chimpanzee divergence supports the notion that changes in transcriptional regulation have contributed to the recent human evolution.
	Method A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements Guandong Wang, Weixiong Zhang Genome Biology 2006, 7:R49 (20 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary WordSpy, a novel, steganalysis-based approach for genome-wide motif-finding is described and applied to yeast and Arabidopsis promoters, identifying cell-cycle motifs.

	Volume 7 Issue 6
	Comment
	Comment The ninth wave Gregory A Petsko Genome Biology 2006, 7:109 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New, all-pervading technologies, such as the web and genomics, are like the 'ninth waves' of surfboard riders, washing over our culture with sudden, transforming power. The danger is that quality is reduced as we deal with the flood of data.
	Review
	Protein family review The MAP1 family of microtubule-associated proteins Shelley Halpain, Leif Dehmelt Genome Biology 2006, 7:224 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MAP1-family proteins are classical microtubule-associated proteins (MAPs) that bind along the microtubule lattice and stabilize microtubules.
	Minireview Protein synthesis molecule by molecule Ido Golding, Edward C Cox Genome Biology 2006, 7:221 (20 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Even a seemingly uniform culture of bacteria is made up of cells very different from each other in terms of their levels of a given protein. This individuality has now finally been quantified at single-molecule resolution.
	Minireview The subcellular localization of the mammalian proteome comes a fraction closer Jeremy C Simpson, Rainer Pepperkok Genome Biology 2006, 7:222 (23 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study shows the successful application of protein correlation profiling to the subcellular localization of organelle proteins in mammalian cells.
	Minireview The elusive yeast interactome Johannes Goll, Peter Uetz Genome Biology 2006, 7:223 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two comprehensive studies of the total complement of protein complexes in yeast come up with surprisingly different answers.
	Opinion Viruses take center stage in cellular evolution Jean-Michel Claverie Genome Biology 2006, 7:110 (16 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Advances in genomics have stimulated new hypotheses that DNA viruses were the origin of the eukaryotic cell nucleus, and that they should be considered as living things.
	Report
	Meeting report Is there gold at the top of the beanstalk? Michael A Djordjevic, Charles Buer Genome Biology 2006, 7:318 (23 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 3rd International Legume Genetics and Genomics Conference, Brisbane, Australia, 9-13 April 2006.
	Meeting report Chromatin remodeling and genome stability Gráinne Barkess Genome Biology 2006, 7:319 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 12th Tenovus Scotland Symposium 'Stability and Regulation of Genes and Genomes', Glasgow UK, 6-7 April 2006.
	Meeting report Mobile DNA: genomes under the influence Cédric Feschotte, Ellen J Pritham Genome Biology 2006, 7:320 (30 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the American Society for Microbiology Conference on Mobile DNA, Banff, Canada, 24 February-1 March 2006.
	Research
	Research Analysis of gene expression in operons of Streptomyces coelicolor Emma Laing, Vassilis Mersinias, Colin P Smith, Simon J Hubbard Genome Biology 2006, 7:R46 (2 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the relative transcript levels of intra-operonic genes in Streptomyces coelicolor suggests significant levels of internal regulation.
	Research Slow, stochastic transgene repression with properties of a timer Clifford L Wang, Desirée C Yang, Matthias Wabl Genome Biology 2006, 7:R47 (9 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The dynamics of retroviral transgene repression were analyzed in several clones; repression was found to be slow and different genomic positions showed different dynamics.
	Research What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Diana Ekman, Sara Light, Åsa K Björklund, Arne Elofsson Genome Biology 2006, 7:R45 (16 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of hubs (proteins with many interactors) and non-hubs in the S. cerevisiae protein interaction network shows that hub proteins are enriched with multiple and repeated domains.
	Research Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling Daniel E Zak, Haiping Hao, Rajanikanth Vadigepalli, Gregory M Miller, Babatunde A Ogunnaike, James S Schwaber Genome Biology 2006, 7:R48 (19 June 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A systems level analysis of circadian time-dependent signaling via the epidermal growth factor receptor in the suprachiasmatic nucleus suggests several transcription factors that mediate the transcriptional response to epidermal growth factor receptor signaling.
	Research Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system Lyris MF de Godoy, Jesper V Olsen, Gustavo A de Souza, Guoqing Li, Peter Mortensen, Matthias Mann Genome Biology 2006, 7:R50 (19 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A mass spectrometry analysis of the yeast proteome shows that complex mixture analysis is not limited by sensitivity but by a combination of dynamic range and by effective sequencing speed.
	Research Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses Nalini Polavarapu, Nathan J Bowen, John F McDonald Genome Biology 2006, 7:R51 (28 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification and characterization of 42 families of chimpanzee endogenous retroviruses and a comparison to their human orthologs is described.
	Research Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence Ian J Donaldson, Berthold Göttgens Genome Biology 2006, 7:R52 (29 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-wide identification of conserved candidate transcription-factor binding sites that have evolved since the human-chimpanzee divergence supports the notion that changes in transcriptional regulation have contributed to the recent human evolution.
	Method A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements Guandong Wang, Weixiong Zhang Genome Biology 2006, 7:R49 (20 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary WordSpy, a novel, steganalysis-based approach for genome-wide motif-finding is described and applied to yeast and Arabidopsis promoters, identifying cell-cycle motifs.

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Volume 7 Issue 6

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